Differential gene expression is the process by which cells become specialized and an organism develops. During embryogenesis, genes must be upregulated or downregulated in order to change the structure and function of the cell, but if all cells have the same genomic information, how do many distinct cells lines arise?
Development is mediated spatially and temporally by the regulatory apparatus. This is made up of the Cis-Regulatory elements — regions of non-coding DNA which regulate the transcription of genes on the same DNA molecule — and the trans-regulatory elements, also known as the regulatory state of the cell, which is defined by the presence and activity of all diffusible transcription factors in the cell. The regulatory state of the cell can be changed by altering expression of transcription factors through signaling pathways. It is the regulatory genome that determines the cell-fates based on the different combinations of these interactions, there is a unique regulatory output for unique combinations of transcription factors. These inputs and outputs form a network which we can reverse engineer.
We are focusing on gastrulation in S. purpuratus embryos; up to this point development is extremely similar in almost all organisms. Before this stage the embryo is composed of a continuous sheet of epithelial cells, which then fold inward, differentiate, and divide to establish a multilayered structure with many distinct cell lines. In Deuterostomes (which both humans and the purple sea urchin are part of) the blastopore becomes the anus and soon develops into the Archenteron, from which the through gut shall arise. It is this point of gastrulation, 30 hours post fertilization, that we have gene expression data for; we will be looking at differences in gene expression between Archenteron cells and the rest of the embryo in order to deduce what genes are being differentially expressed and therefore responsible for the development of the Archenteron.
There were two aims to this internship, firstly, to familiarize myself with differential gene expression and statistics methods for this analysis, in order to identify significant genes in the data provided by Dr Barsi. Secondly, was to learn and understand how Gene Regulatory Networks are characterized, and what research is required for this. The goal of this internship was not to follow the necessary steps to accurately model the GRN for Archenteron development, this has been more centred around identifying potential linkages and learning about the science by using the models and data provided as well as pulling together literature available online.
For the study of embryogenesis and the gene regulatory networks that control the development of the various cell types and regions, there are various model organisms that are used, each with their owns advantages and disadvantages. The purple sea urchin has been used since very early on in the field of developmental biology due to its unique characteristics which have made it useful not only in early research centuries ago but still now in the latest studies.
For example, they share a closer phylogenetic relationship with us than other common invertebrate models such as C. elegans and D. melanogaster; we have many genetic tools for studying them and we understand a lot about their development in terms of gene expression and signalling pathways due to having the full sequenced genome of S. purpuratus; as commercially fished organisms, we have extensive data on their growth, lifespans, reproductive patterns and susceptibility to disease; they are easy to propagate in the lab and the embryos are transparent making them ideal for monitoring development.
Arguably their most important trait is their DNA repair mechanism, which enables researchers to generate transgenic sea urchin embryos using Bacterial Artificial Chromosomes. When BACs are injected into S. purpuratus zygotes before the first division, every cell of the embryo will be transgenic (chimeric embryos can also be generated if integration of foreign DNA does not occur until after the first division). In other species, highly specialized and expensive techniques such as CRISPR would be required, whereas transgenic sea urchins can be made much more efficiently. (Buckley, Dong, Cameron, & Rast, 2018)
Links
Barsi Lab: https://barsi-leidenfrost.org/
People at Barsi Lab: https://barsi-leidenfrost.org/people
Bermuda Institute of Ocean Sciences: http://www.bios.edu/#!/who-we-are
Bermuda Program: http://www.bios.edu/education/bermuda-program
BIOS & Barsi Lab Internship 2021 